MolNFT v2 · #178547 · protein
PHGDH covalently linked to oridonin
7DKM: “PHGDH covalently linked to oridonin”. X-ray diffraction at 1.7, 4 ligands (NAD, ODN, NA). MolNFT v2 #178547 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DKM
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Homo sapiens
- UniProt
- O43175
- Ligands
- NAD, ODN, NA, CL
Structure
x-ray diffraction · resolution 1.7 · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | — | protein | 306 | — | O43175 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ODN · (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14r, 16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one · ligand · chains A
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 7DKM · Phgdh covalently linked to oridonin · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O43175
- Elsewhere: RCSB PDB 7DKM · PDBe 7DKM · UniProt O43175
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